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        <H2><font face="VERDANA,ARIAL,HELVETICA">X!Tandem Viewer</font></H2>
        <font face="VERDANA,ARIAL,HELVETICA">
            X!Tandem Viewer is a graphical user interface for displaying and
            analyzing MS/MS XML result files from <a href="http://www.thegpm.org/TANDEM/">X!Tandem Software</a>.
            <br><br>
            The viewer uses the XTandem Parser library to extract information
            from the XML file. The data are stored into an object model for
            further analysis. X!Tandem Viewer has three different view panels:
            <ol>
                <li><u>The Spectra Files panel:</u> <br>In this view the spectra are listed with spectrum number,
                    filename, precursor m/z, charge and the boolean value, if there was an identification
                    found in the spectrum. When a a row is selected, the other two panels are updated.
                    Sorting the table can be done by clicking on the column headers.</li>
                <li><u>The Spectrum panel:</u><br> The spectrum is displayed with ion annotations.
                    On the x-axis stands the m/z and on the y-axis the intensity. The precursor m/z is
                    depicted below the spectrum. There are checkboxes available for the different
                    types of ions (b and y ions for example). When these checkboxes are selected,
                    each ion type and number can be seen above a certain peak in the spectrum.
                    Below the spectrum each peak is listed in detail  with number, m/z and intensity.</li>
                <li><u>The Identification panel:</u><br> Each identification is listed with number,
                    sequence, modified sequence, start position, end position, experimental mass, theoretical mass,
                    E-value and accession number. In the legend modifications can be found with mass shift at a
                    certain amino acid as referenced in the X!Tandem output XML file. Both fixed and variable modifications
                    are supported and are listed together in the viewer.</li>
            </ol>
            Exporting spectra data is possible via the Export menu. By doing this the data are stored
            in tab delimited text files.
            <br><br>
            <b>Note that the spectra displayed in the X!Tandem Viewer are not the real spectra
            (these are not available in the X!Tandem result files), but rather a histogram representation of
            the spectrum. This is why all spectra have a maximum intensity of 100. The real spectrum is
            found in the corresponding pkl file used as input for the search.</b>
            <br><br>
            For any further questions, feel free to contact the author:
            <a href="mailto:thilo.muth@uni-jena.de">Thilo.Muth@uni-jena.de</a></font>
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